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- PDB-8j5j: The crystal structure of bat coronavirus RsYN04 RBD bound to the ... -

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Basic information

Entry
Database: PDB / ID: 8j5j
TitleThe crystal structure of bat coronavirus RsYN04 RBD bound to the antibody S43
Components
  • Spike protein S1
  • nano antibody S43
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 ...Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesBetacoronavirus sp.
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhao, R.C. / Niu, S. / Han, P. / Qi, J.X. / Gao, G.F. / Wang, Q.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82225021 China
CitationJournal: Zool.Res. / Year: 2023
Title: Cross-species recognition of bat coronavirus RsYN04 and cross-reaction of SARS-CoV-2 antibodies against the virus.
Authors: Zhao, R. / Niu, S. / Han, P. / Gao, Y. / Liu, D. / Luo, C. / Liu, H. / Liu, B. / Xu, Y. / Qi, J. / Chen, Z. / Shi, W. / Wu, L. / Gao, G.F. / Wang, Q.
History
DepositionApr 23, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike protein S1
E: nano antibody S43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8453
Polymers40,6232
Non-polymers2211
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-3 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.373, 68.373, 240.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Spike protein S1


Mass: 24849.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betacoronavirus sp. / Production host: Homo (humans) / References: UniProt: A0A8F0ZU44
#2: Antibody nano antibody S43


Mass: 15773.548 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Homo sapiens (human)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium nitrate, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3→66 Å / Num. obs: 21699 / % possible obs: 99.8 % / Redundancy: 13.9 % / Biso Wilson estimate: 43.9 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.3
Reflection shellResolution: 3→3 Å / Rmerge(I) obs: 1.819 / Num. unique obs: 2255

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→27.55 Å / SU ML: 0.3464 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7088
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 2155 9.96 %
Rwork0.2272 19480 -
obs0.2275 21635 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.97 Å2
Refinement stepCycle: LAST / Resolution: 3→27.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 14 0 2500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432567
X-RAY DIFFRACTIONf_angle_d0.76583487
X-RAY DIFFRACTIONf_chiral_restr0.0487362
X-RAY DIFFRACTIONf_plane_restr0.0075454
X-RAY DIFFRACTIONf_dihedral_angle_d14.7675916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.311270.32471163X-RAY DIFFRACTION90.53
3.07-3.150.29611420.29571303X-RAY DIFFRACTION98.63
3.15-3.230.27351480.27981309X-RAY DIFFRACTION100
3.23-3.330.36831460.27031326X-RAY DIFFRACTION100
3.33-3.430.29951460.26621305X-RAY DIFFRACTION99.93
3.43-3.560.24441460.2571318X-RAY DIFFRACTION99.93
3.56-3.70.31121410.24911284X-RAY DIFFRACTION99.86
3.7-3.870.22051470.2161321X-RAY DIFFRACTION100
3.87-4.070.20681440.20011306X-RAY DIFFRACTION99.86
4.07-4.320.18391480.18591312X-RAY DIFFRACTION99.86
4.32-4.660.16431370.16561296X-RAY DIFFRACTION99.58
4.66-5.120.1841490.18381307X-RAY DIFFRACTION100
5.12-5.860.20141480.21011306X-RAY DIFFRACTION100
5.86-7.350.20151480.23511305X-RAY DIFFRACTION100
7.36-27.550.23331380.23661319X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.28767223657-0.730901112859-2.890525018616.286463205630.4900899502242.63265669775-0.07403084587730.625947753530.976220018845-0.6187375001150.508988324026-0.719381033994-0.914037947890.504293741756-0.3884197056090.584280046288-0.323055914028-0.03006705705580.5287016593320.09937288223960.408866570878-2.25355931835-0.330166574355-10.2198381396
23.929001711-0.707265117776-1.307337182015.96776199991-0.2923357976514.60389668698-0.01356813066670.2675224931540.283250894439-0.4490425639450.0364326518750.00767632215632-0.2315683590120.195898028154-0.01518565291210.277191729927-0.118686763553-0.05258785290530.2713096444040.06957343724990.149511894679-9.59362014679-7.28244148787-14.8726341729
33.186616602030.0523715229072.084916351736.133213476020.2549126392353.048076665910.1018530393810.0099994736288-0.420033348034-0.1115756360140.0627560978414-0.4567670964060.9155754818440.319680640612-0.09746345674760.4148701243550.01203223085320.01022815617970.2302609367780.0003176103920560.22249467625-5.75427961969-26.5876185553-11.0338039314
42.437423213741.23931984961-1.457507689142.28351078934-0.2879070474253.502851707470.673333638118-0.06946060548591.04520588795-0.253274314262-0.199660112263-0.127874698363-1.19062574078-0.0896562244486-0.444153577180.57393686588-0.127731734755-0.06081231637560.2814420000790.05376385108040.400676785709-11.12019493633.41091620085-7.56523954659
54.45922548986-1.161298002921.678646669893.56736080763-0.0143169164025.377113625130.2420799293590.154356423177-0.474858054381-1.02507204631-0.3352469032720.7908733755011.35222076915-0.1450804953740.05434978482590.643297924656-0.04477888603870.02207249969430.308059234128-0.04800038671980.273277234851-19.6647712824-5.61202981814-44.8101707888
65.05775537841.938724308792.642734489712.96341829526-3.29358843179.74264228603-0.193570110183-0.418369362186-0.920856754176-0.535959274117-0.2572577159331.128076460091.31576498808-1.120908303570.2201096494590.830028679062-0.200073168734-0.06104568948210.5732800836870.1599329851250.991148936938-28.3624236239-12.4960381799-28.5377138612
77.104290563760.642468991713-2.289378235157.2074691648-2.645312597318.06616455899-0.0471330567274-0.009767275999330.189796682651-0.6718121424420.109584267031-0.6753459018091.322636826420.5929502657430.04929064257310.695956034765-0.0044104643758-0.06202249313980.2798523054580.04701163494930.25689879158-10.9669824911-6.90662127667-35.446094341
84.77876498579-0.901823027325-3.511723947824.13603585071-2.383763018338.174181636110.0275459035916-0.1320514071350.273728518989-0.4071589875380.02936948332210.00141518956584-0.05517741457510.431224050740.1468823577750.513515454963-0.0940998136487-0.0961758189720.1622224550450.0281864220390.281932284561-16.77302462861.58263170816-30.6737305892
92.32889228005-3.015931008851.438602442065.61611430085-1.980832827297.201161110120.4737250756360.384054620544-0.159801710876-0.318737715767-0.3585803120030.5184406414120.268067633191-0.4801460274370.02316107178960.579668117169-0.0860963448898-0.095899294930.116408528171-0.08257086164250.345272654297-18.9923252744-1.60345406907-38.7186975681
102.62851321388-3.146662714320.554591461453.555353603580.01666867216067.47047386393-0.19230165278-0.0715680405155-0.125915236218-0.267968410934-0.454344440214-0.1011486457510.531918839376-0.3052714543870.06248610082850.473232213143-0.114232331831-0.02616803430110.2067736370490.03352888978360.371324072175-17.6208958216-2.52805188049-22.3603773593
112.02494551611-2.094205595840.6310694015022.79033470229-0.8874208161256.593548914910.2817699331790.222898501815-0.126267373294-0.986206315834-0.2245980632450.1795200093091.086144424310.5010167295040.05101475726380.735593116249-0.0299340626991-0.03123668553640.3509856054880.08740804846460.297052688394-12.2032305526-8.71837004682-38.5687361193
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 55 )AA17 - 551 - 39
22chain 'A' and (resid 56 through 129 )AA56 - 12940 - 113
33chain 'A' and (resid 130 through 184 )AA130 - 184114 - 168
44chain 'A' and (resid 185 through 208 )AA185 - 208169 - 192
55chain 'E' and (resid 21 through 42 )EC21 - 421 - 22
66chain 'E' and (resid 43 through 49 )EC43 - 4923 - 29
77chain 'E' and (resid 50 through 63 )EC50 - 6330 - 43
88chain 'E' and (resid 64 through 81 )EC64 - 8144 - 61
99chain 'E' and (resid 82 through 117 )EC82 - 11762 - 97
1010chain 'E' and (resid 118 through 128 )EC118 - 12898 - 108
1111chain 'E' and (resid 129 through 145 )EC129 - 145109 - 125

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